This may be a rhetorical question, but why can't SharePoint url-encode filenames so it can accept files with any characters?
File named "My File: Has symbols... & stuff.ppt"
would become "My%20File%3A%20Has%20symbols...%20%26%20stuff.ppt" < and that works fine in a URL.
Many other modern web apps handle this, and there are URL encoder/decoder functions readily available. So why does SharePoint not do this?
It's not clear to me what issue you're having... SharePoint (technically IIS) handles URL encoded URLs and as you've said when you URL encode a URL SharePoint accepts it.
Perhaps I'm misunderstanding you. Please let me know.
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